Rfast
### **Version 2.0.8 - Poseidon**
***
> **Improved** (_**by speed, correctness or options**_)
>
> | Function | What's new! |
> | ------------------- | ------------------------------- |
> | colMads | Supports data.frame |
> | colShuffle | Supports data.frame |
> | colMedian | Supports data.frame |
> | colRanks | Supports data.frame and fix bug about method "min". |
> | colSort | Supports data.frame |
> | colMaxs | Supports data.frame |
> | colMins | Supports data.frame |
> | colMinsMaxs | Supports data.frame and add extra option for parallelism. |
> | colrange | Supports data.frame and add extra option for parallelism. |
> | checkExamples | Add extra option for running examples inside environment. Treat special functions with new export attribute. |
> | sort_mat | Depricated. |
>
>
> **LinkingTo** (_**by speed, correctness or options**_)
>
> | Function/Structure | What's new! |
> | ------------------- | ------------------------------- |
> | colMads | Supports data.frame |
> | colShuffle | Supports data.frame |
> | colMedian | Supports data.frame |
> | colSort | Supports data.frame |
> | colMaxs | Supports data.frame |
> | colMins | Supports data.frame |
> | colMinsMaxs | Supports data.frame and add extra option for parallelism. |
> | NA | A structure for manage R's NA values. Supports {int, double, bool, string}. |
> | Type | A structure for manage R's types. Supports {REAL,INT,CHAR,FACTOR,LIST,DATAFRAME}. |
>
> ### **Comments**
***
> From now on all the function will be inside namespace Rfast. Sub-namespaces "vector" and "matrix" have been removed.
>
>
### **Version 2.0.7 - Zeus**
***
> **Improved** (_**by speed, correctness or options**_)
>
> | Function | What's new! |
> | ------------------- | ------------------------------- |
> | colVars | Supports data.frame |
> | colmeans | Supports data.frame |
> | invdir.mle | A small optimization |
### **Version 2.0.6**
***
> **Improved** (_**by speed, correctness or options**_)
>
> | Function | What's new! |
> | ------------------- | ------------------------------- |
> | Dist(method = "bhattacharyya") | Minor optimization. |
### **Version 2.0.5**
***
> **Improved** (_**by speed, correctness or options**_)
>
> | Function | What's new! |
> | ------------------- | ------------------------------- |
> | Dist, total.dist, vecdist | New distance algorithm named "haversine". |
> | gaussian.nb | 3 times faster than the old version. Add new option for parallel which decreases execution 18 times. |
> | checkUsage | Fix a bug about "=function". Optimized empty return values and error messages. |
> | checkAliases, checkTF | Optimized empty return values. |
> | edist | Fix a bug. |
> | dirimultinom.mle | Fix a bug. |
### **Version 2.0.4**
***
> **Improved** (_**by speed, correctness or options**_)
>
> | Function | What's new! |
> | ------------------- | ------------------------------- |
> | nth | Fix a bug using na_rm. In github is #52. |
> | colsums,rowsums | Add new option for removing NAs and optimize option indices. |
### **Version 2.0.0**
***
> **Improved** (_**by speed, correctness or options**_)
>
> | Function | What's new! |
> | ------------------- | ------------------------------- |
> | Var | Time improvement for removing NAs.|
> | checkUsage | From now on check for S3methods and fix bug. |
> | Tcrossprod | Same as R's tcrossprod. |
> | Crossprod | Same as R's crossprod. |
> | matrix_multiplication | Add new arguments for perfoming cross or tcross product. |
### **Version 1.9.9**
***
> **Improved** (_**by speed, correctness or options**_)
>
> | Function | What's new! |
> | ------------------- | ------------------------------- |
> | Var | Time improvement for removing NAs.|
> | colVars | Time improvement and depricate argument "suma".|
> | rowVars | Time improvement and depricate argument "suma".|
> | rowMedians | Add option for removing NAs if any.|
> | colMads | Add option for removing NAs if any, add option for choosing method, fix bug and time improvement.|
> | rowMads | Add option for removing NAs if any, add option for choosing method, fix bug and time improvement.|
> | mad2 | Deprecated. Use "Mad" instead.|
> | med | Deprecated. Use "Median" instead.|
> | colShuffle | Fix a bug.|
> | rowShuffle | Fix a bug.|
> | rmdp | Fix a bug.|
> | checkUsage | From now on check for S3methods. |
> | AddToNamespace | From now on export S3methods. |
> | checkAliases | From now on check the S3methods. |
> | checkNamespace | Don't use it for now. |
>
>
> ### **Comments**
***
> From now on the Rfast can be used in C++ via "LinkingTo" mechanism.
> The main namespace is "Rfast". Inside "Rfast" you will find two more namespaces, "vector" and "matrix".
> Namespace "vector" for calling functions using an Rcpp's or RcppArmadillo's vector.
> Namespace "matrix" for calling functions using an Rcpp's or RcppArmadillo's matrices.
> The signatures of the functions and the arguments are the same that are exported in R.
>
> For namespace "vector" the functions that are available are
>
> - median(x)
> - var(x, std = false, na_rm = false)
> - mad(x, method = "median", na_rm = false)
> - shuffle(x,engine = Engine(time(0)) // Engine by default is default_random_engine. You can use anyone from C++.
>
> For namespace "matrix" the functions that are available are
>
> * transpose(x)
> * matrix_multiplication(x,y)
> * colSort(x, descend = false, stable = false, parallel = false)
> * rowSort(x, descend = false, stable = false, parallel = false)
> * is_symmetric(x)
> * colMedian(x, na_rm = false, parallel = false)
> * rowMedian(x, na_rm = false, parallel = false)
> * colVars(x, std = false, na_rm = false, parallel = false)
> * rowVars(x, std = false, na_rm = false, parallel = false)
> * colMads(x, method = "median", na_rm = false, parallel = false)
> * rowMads(x, method = "median", na_rm = false, parallel = false)
> * colShuffle(x,engine = Engine(time(0)) // Engine by default is default_random_engine. You can use anyone from C++.
> * rowShuffle(x,engine = Engine(time(0)) // Engine by default is default_random_engine. You can use anyone from C++.
>
> How to use it
>
> 1. Just add in "LinkingTo" in your NAMESPACE file the "Rfast" or in Rstudio add in the file "//[[Rcppdepends(Rfast)]]".
>
>
> Include in your cpp files the header "Rfast.h" and enjoy!
### **Version 1.9.8**
***
> **Improved** (_**by speed, correctness or options**_)
>
> | Function | What's new! |
> | ------------------- | ------------------------------- |
> | spml.mle | Fix of a bug. |
> | dirknn | Time improvement. |
> | glm_logistic | Made the code more robust. |
> | vmf.mle | Made the code more robust. |
> | cor.fbed | Fix of a bug. |
> | Dist | Fix of a bug. |
### **Version 1.9.4**
***
>
> **Improved** (_**by speed, correctness or options**_)
>
> | Function | What's new! |
> | ------------------- | ------------------------------- |
> | allbetas | Time improvement |
> | cor.fbed | Time improvement |
> | cor.fsreg | Time improvement |
> | omp | Time improvement |
> | ompr | Time improvement |
> | score.betaregs | Time improvement |
> | score.gammaregs | Time improvement |
> | score.glms | Time improvement |
> | score.invgaussregs | Time improvement |
> | score.negbinregs | Time improvement |
> | score.ztpregs | Time improvement |
> | group.any | Deprecated and replaced by group |
> | group.all | Deprecated and replaced by group |
> | group.min | Deprecated and replaced by group |
> | group.max | Deprecated and replaced by group |
> | group.min_max | Deprecated and replaced by group |
> | group.mean | Deprecated and replaced by group |
> | group.med | Deprecated and replaced by group |
> | group.mad | Deprecated and replaced by group |
> | group.var | Deprecated and replaced by group |
> | group.sum | Deprecated and replaced by group |
> | groupcolVars | Deprecated and replaced by "Rfast2colGroup(...,method="var")" |
> | sort_mat | Deprecated and replaced by "colSort" and "rowSort" |
> | AddToNamespace | remove unused option |
> | nth | fix bug |
### **Version 1.9.3**
***
> **Improved** (_**by speed, correctness or options**_)
>
> | Function | What's new! |
> | ------------------- | ----------------------------------------- |
> | omp | Time improvement. |
> | sort_mat | Replaced by "colSort" and "rowSort" and will be removed in the next udate. |
> | checkUsage | Remove uneccessary option. |
> | read.examples | Remove uneccessary option. |
> | checkTF | Remove uneccessary option. |
> | checkAliases | Remove uneccessary option. |
> | comb_n | Add option for return list or matrix. |
> | rownth | Fix of a bug. |
>
>
> **New**
>
> | Function | What's new! |
> | ------------------- | ----------------------------------------- |
> | omp | Multinomial regression now added. |
> | omp | Option to standardise the predictor variables. |
> | cor.fbed | Option to standardise the predictor variables. |
> | cor.fsreg | Option to standardise the predictor variables. |
> | el.test2 | Empirical likelihood test for two sample means. |
### **Version 1.9.2**
***
> **Improved** (_**by speed, correctness or options**_)
>
> | Function | What's new! |
> | ------------------- | ----------------------------------------- |
> | omp | Time improvement. |
> | ompr | Time improvement. |
> | cor.fbed | Time improvement. |
> | multinom.mle | Time improvement. |
> | weib.reg | Fix a bug and time improvement. |
> | spatmed.reg | Time improvement. |
> | invgauss.reg | Time improvement. |
> | invgauss.regs | Time improvement. |
> | gammareg | Time improvement. |
> | gammaregs | Time improvement. |
> | gammacon | Time improvement. |
> | colvm.mle | Time improvement. |
> | gammaregs | Time improvement. |
> | el.test1 | Time improvement. |
> | Norm | Fix a bug. |
> | which_isFactor | Removed and replaced by "which.is". |
> | checkUsage | Fix a bug. |
> | colsums | Time improvement for integer matrices. |
> | rowsums | Time improvement for integer matrices. |
> | med | Faster **version.|**
> | sort.unique.length | slightly faster **version.|**
> | sort.unique | slightly faster **version.|**
> | Stack | Fix a bug and add function clear for efficient reuse of the Stack. |
> | read.example | Fix a bug. |
>
>
> **New**
>
> | Function | What's new! |
> | ------------------- | ----------------------------------------- |
> | omp | Multinomial regression now added. |
>
> ### **Comments**
>***
> From now on the Rfast needs R **version >= 3.5**
>
### **Version 1.9.1**
***
>
> **Improved** (_**by speed, correctness or options**_)
>
> | Function | What's new! |
> | ------------------- | -------------------- |
> | ompr | Time improvement. |
> | omp | Time improvement . |
> | cholesky | Time improvement. |
> | colnth, rownth | Add extra options, "na.rm" and "descending" order and "index.return". |
> | colrow.zero | deprecate it and replaced by "colrow.value". |
>
>
>
> **New**
>
> | Function | What's new! |
> | ---------------- | --------------------------------------- |
> | which.is | The same with which_isFactor but general. Use this instead of which_isFactor. |
> | colrow.value | Search if a column and row is filled with a specific value. |
### **Version 1.9.0**
***
> **Improved** (_**by speed, correctness or options**_)
>
> | Function | What's new! |
> | ---------------- | ----------------- |
> | topological_sort | Time improvement. |
> | permcor | Fix a bug. |
> | omp | Time improvement. |
> | normlog.regs | Fix a bug. |
> | cova | Added an extra argument. |
> | ompr | Time improvement. |
> | as_integer | Fix a bug. |
> | Round | Fix a bug. digit argument can be up to 15. |
> | matrix.sum | Deprecate it. |
> | countNA | Deprecate it. |
> | sort_unique.length | Deprecate it for numeric numbers. |
> | Rank | Deprecate method="first". |
> | Match | Improved. |
> | nth | Improved method for integers. |
> | colshuffle | Fix a bug. |
> | transpose | Now can handle generic matrix using parallel|
> | colshuffle | Fix a bug. |
>
>
> **New**
>
> | Function | What's new! |
> | ---------------- | ------------------------------------------------------------- |
> | betabinom.mle | MLE of the beta binomial distribution. |
> | betageom.mle | MLE of the beta geometric distribution. |
> | multivt.mle | MLE of the multivariate t distribution. |
> | colpoisson.anovas | Column-wise ANOVA with Poisson distribution. |
> | colquasipoisson.anovas | Column-wise ANOVA with quasi Poisson. |
> | exact.ttest2 | Exact permutations 2-sample t-test. |
> | chi2Test | Chi-squared test of independence. |
> | gchi2Test | G-square and Chi-square tests of indepdence. |
> | chi2tests | Many chi-squared tests of independence. |
> | chi2Test_univariate | Matrix with chi-square tests of indepedence. |
> | mvlnorm.mle | MLE of the multivariate lognormal distribution. |
> | poly.cor | Polychoric correlation. |
> | pooled.cov | Pooled covariance matrix. |
> | spatmed.reg | Spatial median (multivariate) regression. |
> | sscov | Spatial sign covariance matrix. |
> | trim.colmeans | Trimmed column-wise means. |
> | trim.rowmeans | Trimmed row-wise means. |
> | eigs.sym | Extract some principal components from a symmetric matrix. |
> | invgauss.regs | Many simple inverse Gaussian regressions with a log link. |
> | invgauss.reg | Inverse Gaussian regression with a log link. |
> | gammaregs | Many simple Gamma regressions with a log link. |
> | gammareg | Gamma regression with a log link. |
> | gammacon | Gamma regression with a constant term only. |
> | Outer | like R's outer. |
> | RemoveFromNamespace | remove exported functions. |
> | Sort.int | fast sorting integer. |
> | colCumMaxs | apply cummax to column. |
> | colCumSums | apply cumsum to column. |
> | colCumMins | apply cummin to column. |
> | colCumProds | apply cumprod to column. |
> | positive | apply method to each positive value. |
> | positive.negative | apply method to each positive and negative value. |
> | negative | apply method to each negative value. |
> | as.Rfast.function | convert an R function to Rfast's equivalent |
> | mat.mult | Generic matrix multiplication using parallel. |
> | checkUsage | checking usage section in Rd files. |
> | Hash | Create Hash object. |
> | Hash.key | Search key or multi key. |
> | apply.condition | Apply method to each column using a condition. Only integers. |
> | Stack | Stack object. See man page. |
> | iterator | iterator object. See man page. |
> | Elem | access element of an iterator object. |
> | print.environment | S3 method for printing environment. |
> | env.copy | deep copy environment. |
> | ufactor | Untyped factor object. See man page. |
### **Version 1.8.8**
***
> **Improved** (_**by speed, correctness or options**_)
>
> | Function | What's new! |
> | ---------------- | ----------------- |
> | rowMedians | Fix a bug |
> | mad2 | Add option handling NAs and fix a bug |
> | prop.regs | Made it more stable. |
> | logistic_only | Made it more stable. |
> | multinom.regs | Fix a bug and removed parallel for safety reasons. |
> | rint.regs | Fix a bug. |
> | univglms | Add the option for quasi Poisson regression |
> | hd.eigen | Now returns eigen-vectors as well. |
> | ompr | Fix a bug. |
> | tobit.mle | Made it faster. |
> | standardise | Made it faster. |
> | auc | Made it faster. |
> | colaucs | Made it faster. |
> | pc.skel | Made it faster and added more utilities. |
> | cor.fsreg | Made it faster and fix a bug. |
> | allttests | Made it faster and fix a bug. |
> | data.frame.to_matrix | Add option setting colnames and rownames. Fix a bug |
> | nth | Add option for handling NAs. |
> | Pmax | Add option for handling NAs. |
> | Pmin | Add option for handling NAs. |
> | Sort | Add option for handling NAs. |
> | Table | Add option for handling NAs, add option for second argument, deprecate argument as.vector and replaced from "names". |
> | Round | Fix a bug. |
> | Norm | Fix a bug. |
> | colsums | Add option for sum using specific indices. |
> | rowsums | Add option for sum using specific indices and option for parallel. |
> | is_element | Fix a bug. |
> | eachrow | Deprecate argument suma and replaced from argument method. |
> | permutation | Deprecate argument all and replaced from nperm. |
> | permutation.next | Deprecate argument all.next and replaced from nperm. |
> | permutation.prev | Deprecate argument all.prev and replaced from nperm. |
> | data.frame.to_matrix | Fix a bug and time improvement. |
> | Rank | Fix a bug for method="first". |
> | Match | fix bug and time improvement. |
> | bc | Estimate the optimal lambda in the Box-Cox transformation. |
> | ar1 | AR(1) model. |
> | colar1 | Many column-wise AR(1) models. |
> | bc | Estimate the optimal lambda in the Box-Cox transformation. |
> | rbing | Random values generation from a special case of the Bingham distribution. |
> | rbingham | Random values generation from the Bingham distribution. |
> | omp | Orthogonal Matching Pursuit allowing many regression models. |
> | yule | Yule's coefficient of colligation. |
> | col.yule | Many column-wise Yule's coefficients of colligation. |
> | cox.poisrat | Test for the ratio of two Poisson means. |
> | col.coxpoisrat | Many column-wise tests for the ratio of two Poisson means. |
> | colPmax | column-wise parallel maxima |
> | colPmin | column-wise parallel minima |
> | freq.max | maximum frequency of a number |
> | freq.min | minimum frequency of a number |
> | Pmin_Pmax | parallel minima-maxima values |
> | Table.sign | counting the positive, negative, zeros and NA values. |
> | topological_sort | Topological sort of a Directed Acyclic Graph (DAG) |
> | countNA | count the NAs |
> | columns | get specific columns from a matrix |
> | rows | get specific rows from a matrix |
> | eachcol.apply | apply a function to each col after the operation |
> | checkTF | checking man files for missing TRUE/FALSE values in examples |